Source code of the manuscript Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells.

Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to mouse embryonic stem cells and embryoid body cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.

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For more details you can read our preprint: https://www.biorxiv.org/content/early/2017/11/10/217554

• /serum_cells/: analysis done on ~100 embryonic stem cells under serum conditions
• /EB_cells/: analysis done on ~50 embryoid body cells

The raw data is accessible at GEO GSE109262. Parsed data is provided upon request.

• Computational analysis: Ricard Argelaguet ([email protected]) or Andreas Kapourani ([email protected])
• Experimental protocol: Stephen Clark ([email protected])

We have created a Slack group to discuss ideas, suggestions and collaborations about scNMT-seq. This is the link, feel free to join and talk to us!